5VGO | pdb_00005vgo

Bruton's tyrosine kinase (BTK) with compound G-744

PDB DOI: https://doi.org/10.2210/pdb5VGO/pdb

Classification: Transferase/Transferase Inhibitor
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2017-04-11 Released: 2017-07-05
Deposition Author(s): Yu, C., Eigenbrot, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free:
0.184 (Depositor), 0.184 (DCC)
R-Value Work:
0.161 (Depositor), 0.163 (DCC)
R-Value Observed:
0.162 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Discovery of Potent and Selective Tricyclic Inhibitors of Bruton's Tyrosine Kinase with Improved Druglike Properties.

Wang, X., Barbosa, J., Blomgren, P., Bremer, M.C., Chen, J., Crawford, J.J., Deng, W., Dong, L., Eigenbrot, C., Gallion, S., Hau, J., Hu, H., Johnson, A.R., Katewa, A., Kropf, J.E., Lee, S.H., Liu, L., Lubach, J.W., Macaluso, J., Maciejewski, P., Mitchell, S.A., Ortwine, D.F., DiPaolo, J., Reif, K., Scheerens, H., Schmitt, A., Wong, H., Xiong, J.M., Xu, J., Zhao, Z., Zhou, F., Currie, K.S., Young, W.B.

(2017) ACS Med Chem Lett 8: 608-613

PubMed: 28626519 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.7b00103
Primary Citation Related Structures:
5VGO

PubMed Abstract:
In our continued effort to discover and develop best-in-class Bruton's tyrosine kinase (Btk) inhibitors for the treatment of B-cell lymphomas, rheumatoid arthritis, and systemic lupus erythematosus, we devised a series of novel tricyclic compounds that improved upon the druglike properties of our previous chemical matter. Compounds exemplified by G-744 are highly potent, selective for Btk, metabolically stable, well tolerated, and efficacious in an animal model of arthritis.

Organizational Affiliation

Genentech, Inc., Research and Early Development, 1 DNA Way, South San Francisco, California 94080, United States.

Macromolecule Content

Total Structure Weight: 32.93 kDa
Atom Count: 2,605
Modeled Residue Count: 265
Deposited Residue Count: 271
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase BTK	A	271	Homo sapiens	Mutation(s): 0 Gene Names: BTK, AGMX1, ATK, BPK EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q06187 (Homo sapiens) Explore Q06187 Go to UniProtKB: Q06187
PHAROS: Q06187 GTEx: ENSG00000010671
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q06187
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9B1 Query on 9B1 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	2-[2-(hydroxymethyl)-3-{1-methyl-6-oxo-5-[(pyrimidin-4-yl)amino]-1,6-dihydropyridin-3-yl}phenyl]-6,6-dimethyl-3,4,6,7-tetrahydro-2H-cyclopenta[4,5]thieno[2,3-c]pyridin-1(5H)-one C₂₉ H₂₉ N₅ O₃ S QAESSIFTPVEYRY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
PG0 Query on PG0 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	2-(2-METHOXYETHOXY)ETHANOL C₅ H₁₂ O₃ SBASXUCJHJRPEV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
9B1	BindingDB: 5VGO	Ki: 1.3 (nM) from 1 assay(s)
		IC50: min: 2, max: 87 (nM) from 4 assay(s)
		EC50: min: 22, max: 33 (nM) from 2 assay(s)